Fabrice,
As you note that
pathview does not work with Biocarta or Reactome pathways directly at
this
time. You may still work with them if you can parse these pathways
into "graphNEL"
objects (defined in graph package). We may provide this functionality
as an
explicit feature in future release of pathview.
The following
example shows you how to redo the pathview workflow step by step when
you have
pathway data file parsed into a "graphNEL" object (gR1 below). HTH.
Weijun Luo
xml.file=paste(kegg.dir,
"hsa04966.xml", sep="/")
gR1=pathview:::parseKGML2Graph2(xml.file,
genesOnly=FALSE, expand=FALSE, split.group=FALSE)
node.data=node.info(gR1)
plot.data.gene=node.map(mol.data=gse16873.d[,1],
node.data,
node.types="gene")
head(plot.data.gene)
cols.ts.gene=node.color(plot.data.gene,
limit=1, bins=10)
head(cols.ts.gene)
pv.pars=
keggview.graph(plot.data.gene=plot.data.gene,
cols.ts.gene=cols.ts.gene,
node.data=node.data, path.graph=gR1,
pathway.name="hsa04966",
sign.pos="bottomleft")
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